[Biojava-dev] Biojava genome test fails

[Paolo Pavan]

Hi Jose,
Interesting! I'm also working on commit
154edb7f9a5e9e54f25df3e27aeb169b4fab7799 and below is the result. At a
first glance it does not seem a network problem, it downloads
maven-metadata.xml.
What do you think?
Paolo

-------------------------------------------------------
 T E S T S
-------------------------------------------------------
Running org.biojava.nbio.genome.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec -
in org.biojava.nbio.genome.AppTest
Running org.biojava.nbio.genome.FeatureListTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.502 sec -
in org.biojava.nbio.genome.FeatureListTest
Running org.biojava.nbio.genome.GeneFeatureHelperTest
18:04:40 [main] INFO  org.biojava.nbio.genome.parsers.gff.GFF3Reader -
Reading:
C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\src\test\resources\volvox.gff3
18:04:41 [main] INFO  org.biojava.nbio.genome.parsers.gff.GFF3Reader -
Reading: src/test/resources/amphimedon.gff3
18:04:41 [main] INFO  org.biojava.nbio.genome.parsers.gff.GFF3Reader -
Reading:
C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\src\test\resources\volvox.gff3
18:04:41 [main] INFO  org.biojava.nbio.genome.parsers.gff.GFF3Reader -
Reading:
C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\src\test\resources\volvox.gff3
18:04:41 [main] INFO  org.biojava.nbio.genome.GeneFeatureHelperTest - Note
[protein kinase]
18:04:41 [main] INFO  org.biojava.nbio.genome.GeneFeatureHelper - Gene EDEN
found at ctgA 1050 9000 POSITIVE
18:04:41 [main] INFO  org.biojava.nbio.genome.GeneFeatureHelper - Gene
rna-Apple3 found at ctgA 18000 21200 POSITIVE
Tests run: 6, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.598 sec
<<< FAILURE! - in org.biojava.nbio.genome.GeneFeatureHelperTest
testOutputFastaSequenceLengthGFF3(org.biojava.nbio.genome.GeneFeatureHelperTest)
Time elapsed: 0.199 sec  <<< FAILURE!
junit.framework.AssertionFailedError: actual file is shorter
    at junit.framework.Assert.fail(Assert.java:57)
    at junitx.framework.FileAssert.assertBinaryEquals(FileAssert.java:240)
    at
org.biojava.nbio.genome.GeneFeatureHelperTest.testOutputFastaSequenceLengthGFF3(GeneFeatureHelperTest.java:105)


2015-07-14 14:44 GMT+02:00 Jose Manuel Duarte <jose.duarte at psi.ch>:

>  It works for me (on commit 154edb7f9a5e9e).
>
> Could that be some kind of network problem?
>
> Jose
>
>
>
> On 14.07.2015 14:32, Paolo Pavan wrote:
>
>   Hello,
>  It seems that testOutputFastaSequenceLengthGFF3 fails in biojava-genome
> 4.1.1 snapshot.
>  Is this happening to someone else?
>
>  bye bye,
>  Paolo
>
>
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